RetrogeneDB ID: | retro_ecab_224 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 10:78868130..78868566(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HLF | ||
| Ensembl ID: | ENSECAG00000016953 | ||
| Aliases: | None | ||
| Description: | hepatic leukemia factor [Source:HGNC Symbol;Acc:4977] |
Retrocopy-Parental alignment summary:
>retro_ecab_224
CGTCATGACCATAGCCTCCACATTCCCGTAGCCAGCTGCCCAGCTGGCCCTTCTATCCTGGCCCTGACATCTGGGCTCTA
CTCACCCAGCATCCTGTCGCAGAACCGTACACACAATCCCATCAGTCCAGGTCAGCTGCTGTCAGCAAACCACCAGACAT
GGGGCCCATGGATCCTGACAAGATGCAGGTCCCAGTGGGGTACGAGCCAGTTGGGGGAGACCTTGCTCTCTCCAGCATCC
ATGCCCACAAAATATTTGATTCTAGTAAACCCAAGTTCTCTAAGTTTGAACTGAAAGCATAGTCCATGATTAGGAAATCT
CACACAGTCTTCATACCTGGCTGTTGAAATTTAACAAGTACTGAGCTATGATTAGAAAGAACAACACAGCAGCCAAGTGC
TCTTGAGATGCCTGAAGGCTGAGGGAGAAAGAGATT
ORF - retro_ecab_224 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.63 % |
| Parental protein coverage: | 58.75 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QHDHSPHPPGLQPASSAAPSVMDLSSRASAPIHPGIPSPNCMQSPIRPGQLLPANRNT-PSPIDPDTIQV |
| .HDHS.H.P.......A.PS...L....S....P.I.S.N....PI.PGQLL.AN..T...P.DPD..QV | |
| Retrocopy | RHDHSLHIP--VASCPAGPSILALT---SGLYSPSILSQNRTHNPISPGQLLSANHQT<MGPMDPDKMQV |
| Parental | PVGYEPDPADLALSSIPGQEMFDPRKRKFSEEELKPQPMIKKARKVFIPDD-LKDDKYWARRRKNNMAAK |
| PVGYEP...DLALSSI.....FD..K.KFS..ELK...MI.K...VFIP...LK..KY.A..RKNN.AAK | |
| Retrocopy | PVGYEPVGGDLALSSIHAHKIFDSSKPKFSKFELKA*SMIRKSHTVFIPGC<LKFNKY*AMIRKNNTAAK |
| Parental | RSRDARRLKENQI |
| .S.DA.RL.E..I | |
| Retrocopy | CS*DA*RLREKEI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 37 .01 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 50 .06 RPM |
| SRP021940_embryo | 0 .00 RPM | 2 .40 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 1 .49 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 4 .15 RPM |
| SRP021940_testis | 0 .00 RPM | 1 .66 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_224 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_224 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_224 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000016953 | 1 retrocopy |
retro_ecab_224 ,
|
| Tursiops truncatus | ENSTTRG00000007194 | 1 retrocopy |